From b81cd4b32c8411637f31164cc696a471b1074baa Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Mon, 26 Oct 2020 14:23:04 +0100
Subject: Put the legend in its own area for plot.nlme.mmkin

---
 man/nlme.Rd            |  6 +++++-
 man/nlme.mmkin.Rd      |  2 ++
 man/plot.nlme.mmkin.Rd | 20 ++++++--------------
 3 files changed, 13 insertions(+), 15 deletions(-)

(limited to 'man')

diff --git a/man/nlme.Rd b/man/nlme.Rd
index 2ee2a20c..df721a0f 100644
--- a/man/nlme.Rd
+++ b/man/nlme.Rd
@@ -72,8 +72,12 @@ m_nlme <- nlme(value ~ nlme_f(name, time, parent_0, log_k_parent_sink),
   start = mean_dp)
 summary(m_nlme)
 plot(augPred(m_nlme, level = 0:1), layout = c(3, 1))
-# augPred does not seem to work on fits with more than one state
+# augPred does not work on fits with more than one state
 # variable
+#
+# The procedure is greatly simplified by the nlme.mmkin function
+f_nlme <- nlme(f)
+plot(f_nlme)
 
 }
 \seealso{
diff --git a/man/nlme.mmkin.Rd b/man/nlme.mmkin.Rd
index 87d84c74..041b939a 100644
--- a/man/nlme.mmkin.Rd
+++ b/man/nlme.mmkin.Rd
@@ -85,6 +85,7 @@ AIC(f_nlme_sfo, f_nlme_dfop)
 print(f_nlme_dfop)
 plot(f_nlme_dfop)
 endpoints(f_nlme_dfop)
+
 \dontrun{
   f_nlme_2 <- nlme(f["SFO", ], start = c(parent_0 = 100, log_k_parent = 0.1))
   update(f_nlme_2, random = parent_0 ~ 1)
@@ -131,6 +132,7 @@ endpoints(f_nlme_dfop)
     AIC(f_nlme_sfo, f_nlme_sfo_tc, f_nlme_dfop, f_nlme_dfop_tc)
     print(f_nlme_dfop_tc)
   }
+
   f_2_obs <- mmkin(list("SFO-SFO" = m_sfo_sfo,
    "DFOP-SFO" = m_dfop_sfo),
     ds_2, quiet = TRUE, error_model = "obs")
diff --git a/man/plot.nlme.mmkin.Rd b/man/plot.nlme.mmkin.Rd
index 5f6e4ed3..6944d4b1 100644
--- a/man/plot.nlme.mmkin.Rd
+++ b/man/plot.nlme.mmkin.Rd
@@ -7,17 +7,16 @@
 \method{plot}{nlme.mmkin}(
   x,
   i = 1:ncol(x$mmkin_orig),
-  main = NULL,
   obs_vars = names(x$mkinmod$map),
   standardized = TRUE,
   xlab = "Time",
   xlim = range(x$data$time),
-  legends = 1,
-  lpos = "topright",
-  inset = c(0.05, 0.05),
   resplot = c("predicted", "time"),
   ymax = "auto",
   maxabs = "auto",
+  ncol.legend = ifelse(length(i) <= 3, length(i) + 1, ifelse(length(i) <= 8, 3, 4)),
+  nrow.legend = ceiling((length(i) + 1)/ncol.legend),
+  rel.height.legend = 0.03 + 0.08 * nrow.legend,
   rel.height.bottom = 1.1,
   pch_ds = 1:length(i),
   col_ds = pch_ds + 1,
@@ -32,8 +31,6 @@
 \item{i}{A numeric index to select datasets for which to plot the nlme fit,
 in case plots get too large}
 
-\item{main}{The main title placed on the outer margin of the plot.}
-
 \item{obs_vars}{A character vector of names of the observed variables for
 which the data and the model should be plotted. Defauls to all observed
 variables in the model.}
@@ -45,14 +42,6 @@ variables in the model.}
 
 \item{xlim}{Plot range in x direction.}
 
-\item{legends}{An index for the fits for which legends should be shown.}
-
-\item{lpos}{Position(s) of the legend(s). Passed to \code{\link{legend}} as
-the first argument.  If not length one, this should be of the same length
-as the obs_var argument.}
-
-\item{inset}{Passed to \code{\link{legend}} if applicable.}
-
 \item{resplot}{Should the residuals plotted against time or against
 predicted values?}
 
@@ -61,6 +50,8 @@ predicted values?}
 \item{maxabs}{Maximum absolute value of the residuals. This is used for the
 scaling of the y axis and defaults to "auto".}
 
+\item{rel.height.legend}{The relative height of the legend shown on top}
+
 \item{rel.height.bottom}{The relative height of the bottom plot row}
 
 \item{pch_ds}{Symbols to be used for plotting the data.}
@@ -89,6 +80,7 @@ dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"),
   A1 = mkinsub("SFO"), quiet = TRUE)
 f <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE, cores = 1)
 plot(f[, 3:4], standardized = TRUE)
+
 library(nlme)
 # For this fit we need to increase pnlsMaxiter, and we increase the
 # tolerance in order to speed up the fit for this example evaluation
-- 
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